Chicken rRNA Gene Cluster Structure

Abstract

Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5’ETS (1836 bp), 18S rRNA gene (1823 bp), ITS1 (2530 bp), 5.8S rRNA gene (157 bp), ITS2 (733 bp), 28S rRNA gene (4441 bp) and 3’ETS (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity.

Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary

“…The most plausible reason being the excessive enrichment of repetitive sequences and artifacts of the assembly procedures of the genomes. As discussed by Dyomin et al [ 45 ] there is no complete annotation of rRNA genes in avian genomes so far despite all efforts made.…”

The distribution of 45S rDNA sites in bird chromosomes suggests multiple evolutionary histories

“…The rDNA genes are extremely important for cell function, given that they encode the rRNA involved in ribosome biogenesis (Hadjiolov, 1985;Shaw and Brown, 2012). In this process, two rDNA clusters are involved: the 45S rDNA composed by 18S, 5.8S, and 28S genes, and internal (ITS1 and ITS2) and external (5'ETS and 3'ETS) transcribed spacers; and the 5S rDNA, composed by a 5S gene separated by an intergenic spacer region (IGS) (Daniels and Delany, 2003;Dyomin et al, 2016). In the eukaryotic genome, multiple copies of these clusters are organized in tandem in the DNA, forming the 5S and 45S rDNA sites in the chromosome (Daniels and Delany, 2003;Dyomin et al, 2016).…”

Ribosomal RNA gene functioning in avian oogenesis

“…Several attempts have been made to determine the sequences of rDNA arrays and rDNA copy numbers in various chicken breeds and lines (Delany and Krupkin 1999;Delany et al 2009) but the precise number and arrangement of rDNA repeats, including the size and sequences of spacer regions, remain unknown. Most likely, the lack of data on chicken 18S, 5.8S, 28S rRNA precursor structure is related to the specific nature of the rDNA TU organization with the highly GC-rich internal transcribed spacers potentially forming numerous hairpins and blocking polymerase chain reaction (PCR) amplification (Dyomin et al 2016). Poorly represented or even entirely absent rDNA sequences seem to be a common problem of the most currently assembled genomes.…”

“…We refer the interested reader to a review by Shaw and Brown (2012) who emphasized our lack of knowledge of full rRNA sequences in higher eukaryotes because of the imperfection of modern technology for highly repetitive sequence analysis: BWe therefore do not know absolutely whether all the rDNA repeats are intact functional genes or whether other functional sequences are interspersed with them, and it is merely an assumption that all rDNA repeats are potentially transcribable^ (Shaw and Brown 2012). In birds, the small size of the NOR microchromosomes combined with an apparently complicated organization of rDNA repeats (Dyomin et al 2016) impede chromosome structure investigation and sequencing. During the period of oocyte growth all avian chromosomes transform into LBCs, i.e.…”